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Added algorithm files
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7 files changed

+318
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‎src/Core/Algorithms/Legacy/Fields/CMakeLists.txt‎

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@@ -98,6 +98,7 @@ SET(Core_Algorithms_Legacy_Fields_HEADERS
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RegisterWithCorrespondences.h
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SampleField/GeneratePointSamplesFromField.h
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DistanceField/CalculateIsInsideField.h
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CreateMesh/ConvertMatricesToMeshAlgo.h
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)
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SET(Core_Algorithms_Legacy_Fields_SRCS
@@ -119,6 +120,7 @@ SET(Core_Algorithms_Legacy_Fields_SRCS
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#CompareFields/CompareFields.cc
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#CompareFields/SimilarMeshes.cc
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#CreateMesh/CreateMeshFromNrrd.cc
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CreateMesh/ConvertMatricesToMeshAlgo.h
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DistanceField/CalculateDistanceField.cc
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DistanceField/CalculateIsInsideField.cc

‎src/Core/Algorithms/Legacy/Fields/CreateMesh/ConvertMatricesToMeshAlgo.cc‎

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/*
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For more information, please see: http://software.sci.utah.edu
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The MIT License
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Copyright (c) 2015 Scientific Computing and Imaging Institute,
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University of Utah.
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Permission is hereby granted, free of charge, to any person obtaining a
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copy of this software and associated documentation files (the "Software"),
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to deal in the Software without restriction, including without limitation
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the rights to use, copy, modify, merge, publish, distribute, sublicense,
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and/or sell copies of the Software, and to permit persons to whom the
15+
Software is furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included
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in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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DEALINGS IN THE SOFTWARE.
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*/
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#include <Core/Algorithms/Legacy/Fields/FieldData/ConvertMatricesToMeshAlgo.h>
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#include <Core/Datatypes/Legacy/Field/Field.h>
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#include <Core/Datatypes/Legacy/Field/VField.h>
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#include <Core/Datatypes/Matrix.h>
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#include <Core/Datatypes/MatrixTypeConversions.h>
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#include <Core/Datatypes/SparseRowMatrix.h>
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#include <Core/Datatypes/DatatypeFwd.h>
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#include <Core/Datatypes/Legacy/Field/FieldInformation.h>
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#include <Core/Datatypes/DenseMatrix.h>
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#include <Core/Algorithms/Base/AlgorithmVariableNames.h>
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#include <Core/Algorithms/Base/AlgorithmPreconditions.h>
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using namespace SCIRun::Core::Algorithms;
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using namespace SCIRun::Core::Geometry;
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using namespace SCIRun::Core::Algorithms::Fields;
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using namespace SCIRun::Core::Algorithms::Fields::Parameters;
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using namespace SCIRun::Core::Datatypes;
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using namespace SCIRun;
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ALGORITHM_PARAMETER_DEF(Fields, InputFieldTypeName)
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ALGORITHM_PARAMETER_DEF(Fields, InputFieldTypeTypeName)
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ALGORITHM_PARAMETER_DEF(Fields, OutputMeshDataType)
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ALGORITHM_PARAMETER_DEF(Fields, OutputFieldDatatype)
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ConvertMatricesToMeshAlgo::ConvertMatricesToMeshAlgo()
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{
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add_option(Parameters::OutputMeshDataType, "TetVol", "Curve|HexVol|PointCloud|PrismVol|QuadSurf|TetVol|TriSurf");
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add_option(Parameters::OutputFieldDataType, "double", "unsigned char|unsigned short|unsigned int|char|short|int|float|double|Vector|Tensor");
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}
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bool
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ConvertMatricesToMeshAlgo::runImpl(FieldHandle input_field, DenseMatrixHandle input_matrix, FieldHandle& output_field) const
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{/*
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ScopedAlgorithmStatusReporter r(this, "ConvertIndicesToFieldData");
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if (!input_field)
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{
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error("No input field");
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return (false);
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}
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FieldInformation fi(input_field);
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output_field = CreateField(fi);
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FieldInformation fo(output_field);
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if (fi.is_nonlinear())
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{
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error("This function has not yet been defined for non-linear elements");
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return (false);
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}
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if (fi.is_nodata())
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{
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error("This function has not yet been defined for fields with no data");
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return (false);
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}
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if (fi.is_vector() || fi.is_tensor())
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{
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error("This function has not yet been defined for fields with vectors or tensors as indices");
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return (false);
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}
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size_type nrows = input_matrix->nrows();
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size_type ncols = input_matrix->ncols();
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std::string algotype;
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if (ncols == 1)
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{
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algotype = "Scalar";
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}
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else if (ncols == 3)
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{
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algotype = "Vector";
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}
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else if (ncols == 6 || ncols == 9)
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{
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algotype = "Tensor";
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}
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else
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{
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if (nrows == 1)
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{
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algotype = "Scalar";
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}
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else if (nrows == 3)
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{
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algotype = "Vector";
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}
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else if (nrows == 6 || nrows == 9)
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{
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algotype = "Tensor";
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}
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else
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{
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error("Data does not have dimension of 1, 3, 6, or 9");
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return (false);
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}
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}
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if (algotype == "Scalar")
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{
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std::string datatype;
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get_option(Parameters::OutputFieldDataType);
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fo.set_data_type(get_option(Parameters::OutputFieldDataType));
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}
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if (algotype == "Vector") fo.make_vector();
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if (algotype == "Tensor") fo.make_tensor();
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//--------------------------------
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// VIRTUAL INTERFACE
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output_field = CreateField(fo, input_field->mesh());
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VField* vinput = input_field->vfield();
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VField* voutput = output_field->vfield();
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voutput->resize_fdata();
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if (algotype == "Scalar")
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{
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int max_index = input_matrix->nrows() * input_matrix->ncols();
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const double *dataptr = input_matrix->data();
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VMesh::size_type sz = vinput->num_values();
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for (VMesh::index_type r = 0; r<sz; r++)
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{
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int idx;
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vinput->get_value(idx, r);
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if ((idx < 0) || (idx >= max_index))
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{
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error("Index exceeds matrix dimensions");
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return (false);
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}
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voutput->set_value(dataptr[idx], r);
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}
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return (true);
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}
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else if (algotype == "Vector")
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{
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if (input_matrix->ncols() != 3)
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{
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input_matrix.reset(new DenseMatrix(input_matrix->transpose()));
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}
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const double *dataptr = input_matrix->data();
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int max_index = input_matrix->nrows();
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VMesh::size_type sz = vinput->num_values();
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for (VMesh::index_type r = 0; r<sz; r++)
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{
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int idx;
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vinput->get_value(idx, r);
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if ((idx < 0) || (idx >= max_index))
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{
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error("Index exceeds matrix dimensions");
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return (false);
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}
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voutput->set_value(Vector(dataptr[3 * idx], dataptr[3 * idx + 1], dataptr[3 * idx + 2]), r);
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}
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return (true);
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}
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else if (algotype == "Tensor")
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{
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if ((input_matrix->ncols() != 6) && (input_matrix->ncols() != 9))
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{
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input_matrix.reset(new DenseMatrix(input_matrix->transpose()));
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}
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int max_index = input_matrix->nrows();
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const double *dataptr = input_matrix->data();
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int ncols = input_matrix->ncols();
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VMesh::size_type sz = vinput->num_values();
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for (VMesh::index_type r = 0; r<sz; r++)
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{
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int idx;
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vinput->get_value(idx, r);
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if ((idx < 0) || (idx >= max_index))
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{
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error("Index exceeds matrix dimensions");
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return (false);
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}
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if (ncols == 6)
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{
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voutput->set_value(Tensor(dataptr[3 * idx], dataptr[3 * idx + 1], dataptr[3 * idx + 2], dataptr[3 * idx + 3], dataptr[3 * idx + 4], dataptr[3 * idx + 5]), r);
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}
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else
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{
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voutput->set_value(Tensor(dataptr[3 * idx], dataptr[3 * idx + 1], dataptr[3 * idx + 2], dataptr[3 * idx + 4], dataptr[3 * idx + 5], dataptr[3 * idx + 8]), r);
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}
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}
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AlgorithmOutput output;
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output[Variables::OutputField] = output_field;
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return (true);
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}
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// keep the compiler happy:
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// it seems reasonable to return false if none of the cases apply (AK)
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return (false);
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*/
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}
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AlgorithmOutput ConvertMatricesToMeshAlgo::run_generic(const AlgorithmInput& input) const
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{/*
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auto field = input.get<Field>(Variables::InputField);
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auto inputmatrix = input.get<DenseMatrix>(Variables::InputMatrix);
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FieldHandle output_field;
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if (!runImpl(field, inputmatrix, output_field))
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THROW_ALGORITHM_PROCESSING_ERROR("False returned on legacy run call.");
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AlgorithmOutput output;
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output[Variables::OutputField] = output_field;
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return output; */
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}

‎src/Core/Algorithms/Legacy/Fields/CreateMesh/ConvertMatricesToMeshAlgo.h‎

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/*
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For more information, please see: http://software.sci.utah.edu
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4+
The MIT License
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6+
Copyright (c) 2015 Scientific Computing and Imaging Institute,
7+
University of Utah.
8+
9+
10+
Permission is hereby granted, free of charge, to any person obtaining a
11+
copy of this software and associated documentation files (the "Software"),
12+
to deal in the Software without restriction, including without limitation
13+
the rights to use, copy, modify, merge, publish, distribute, sublicense,
14+
and/or sell copies of the Software, and to permit persons to whom the
15+
Software is furnished to do so, subject to the following conditions:
16+
17+
The above copyright notice and this permission notice shall be included
18+
in all copies or substantial portions of the Software.
19+
20+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
21+
OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
22+
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
23+
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
24+
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
25+
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
26+
DEALINGS IN THE SOFTWARE.
27+
*/
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#ifndef CORE_ALGORITHMS_FIELDS_FIELDDATA_CONVERTMATRICESTOMESHALGO_H
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#define CORE_ALGORITHMS_FIELDS_FIELDDATA_CONVERTMATRICESTOMESHALGO_H
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#include <Core/Algorithms/Base/AlgorithmBase.h>
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#include <Core/Algorithms/Legacy/Fields/share.h>
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namespace SCIRun {
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namespace Core {
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namespace Algorithms {
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namespace Fields {
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ALGORITHM_PARAMETER_DEF(Fields, InputFieldTypeName);
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ALGORITHM_PARAMETER_DEF(Fields, InputFieldTypeTypeName);
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ALGORITHM_PARAMETER_DEF(Fields, OutputMeshDataType);
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ALGORITHM_PARAMETER_DEF(Fields, OutputFieldDatatype);
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class SCISHARE ConvertMatricesToMeshAlgo : public AlgorithmBase
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{
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public:
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ConvertMatricesToMeshAlgo();
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bool runImpl(FieldHandle input_field, Datatypes::DenseMatrixHandle input_matrix, FieldHandle& output_field)const;
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// bool runImpl(FieldHandle input, Datatypes::MatrixHandle input_matrix, FieldHandle& output) const;
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virtual AlgorithmOutput run_generic(const AlgorithmInput& input) const override;
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};
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}
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}
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}
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}
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#endif
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‎src/Interface/Modules/Fields/ConvertMatricesToMeshDialog.cc‎

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@@ -27,7 +27,7 @@
2727
*/
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2929
#include <Interface/Modules/Fields/ConvertMatricesToMeshDialog.h>
30-
#include <Core/Algorithms/Legacy/Fields/FieldData/ConvertMatricesToMesh.h>
30+
#include <Modules/Legacy/Fields/ConvertMatricesToMesh.h>
3131
#include <Core/Algorithms/Legacy/Fields/FieldData/ConvertFieldBasisType.h>
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using namespace SCIRun::Gui;

‎src/Modules/Factory/Config/ConvertMatricesToMesh.module‎

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"namespace": "Fields",
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"status": "Ported module",
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"description": "Store/retrieve values from an input matrix to/from the data of a field",
7-
"header": "Modules/Legacy/Forward/ConvertMatricesToMesh.h"
7+
"header": "Modules/Legacy/Fields/ConvertMatricesToMesh.h"
88
},
99
"algorithm": {
10-
"name": "N/A",
11-
"namespace": "N/A",
12-
"header": "N/A"
10+
"name": "ConvertMatricesToMeshAlgo",
11+
"namespace": "Fields",
12+
"header": "Core/Algorithms/Legacy/Fields/CreateMesh/ConvertMatricesToMeshAlgo.h"
1313
},
1414
"UI": {
1515
"name": "ConvertMatricesToMeshDialog",

‎src/Modules/Legacy/Fields/ConvertMatricesToMesh.cc‎

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3535
///
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3737
#include <Modules/Legacy/Fields/ConvertMatricesToMesh.h>
38+
#include <Core/Datatypes/Matrix.h>
3839
#include <Core/Datatypes/Legacy/Field/Field.h>
3940
#include <Core/Datatypes/Legacy/Field/Mesh.h>
40-
#include <Core/Datatypes/Legacy/Matrix/Matrix.h>
4141
#include <Core/Datatypes/Legacy/Field/FieldInformation.h>
4242

4343
using namespace SCIRun::Modules::Fields;
4444
using namespace SCIRun::Dataflow::Networks;
4545

46-
ALGORITHM_PARAMETER_DEF(Fields, InputFieldTypeName)
47-
ALGORITHM_PARAMETER_DEF(Fields, InputFieldTypeTypeName)
48-
ALGORITHM_PARAMETER_DEF(Fields, OutputMeshDataType)
49-
ALGORITHM_PARAMETER_DEF(Fields, OutputFieldDatatype)
46+
const ModuleLookupInfo ConvertMatricesToMesh::staticInfo_("ConvertMatricesToMesh", "NewField", "SCIRun");
5047

51-
ConvertMatricesToMesh::ConvertMatricesToMesh()
52-
: Module(ModuleLookupInfo("ConvertMatricesToMesh", "ChangeMesh", "SCIRun"), false)
48+
ConvertMatricesToMesh::ConvertMatricesToMesh() : Module(staticInfo_)
5349
{
5450
INITIALIZE_PORT(MeshElements);
5551
INITIALIZE_PORT(MeshPositions);

‎src/Modules/Legacy/Fields/ConvertMatricesToMesh.h‎

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@@ -65,6 +65,8 @@ namespace SCIRun {
6565
INPUT_PORT(1, MeshPositions, Matrix);
6666
INPUT_PORT(2, MeshNormals, Matrix);
6767
OUTPUT_PORT(0, OutputField, LegacyField);
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69+
static const Dataflow::Networks::ModuleLookupInfo staticInfo_;
6870
};
6971
}
7072
}

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